closing tag should also be removed from all split XML files and then …

…added to the final XML file. Fixed #17
AgBase · May 18, 2021 · ce5d9e6 · ce5d9e6
1 parent 08ae606
commit ce5d9e6
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/5.45-80-cyverse/iprs_wrapper.sh b/5.45-80-cyverse/iprs_wrapper.sh
@@ -226,11 +226,15 @@ find ./$outdir  -type f -name "query.*.tsv" -print0 | xargs -0 cat -- >> $outdir
 find ./$outdir  -type f -name "query.*.json" -print0 | xargs -0 cat -- >> $outdir/"$inname"'.json'
 
 
-##REMOVE XML HEADERLINES AND CAT FILES TOGETHER
-xmlhead=$(head -n 1 ./$outdir/query.0.xml)
+##REMOVE XML HEADERLINES TAILLINES AND CAT FILES TOGETHER
+xmlhead=$(head -n 1 $outdir/query.0.xml)
+xmltail=$(tail -1 $outdir/query.0.xml)
 find ./$outdir  -type f -name "query.*.xml" -exec sed -i '1d' {} \;
+find ./$outdir  -type f -name "query.*.xml" -exec sed -i '$d' {} \;
 find ./$outdir  -type f -name "query.*.xml" -print0 | xargs -0 cat -- >> $outdir/tmp.xml
 echo -e "$xmlhead" | cat - $outdir/tmp.xml > $outdir/"$inname"'.xml'
+echo -e "$xmltail" >> $outdir/"$inname"'.xml'
+
 
 ##REMOVE GFF# HEADERLINES AND CAT FILES TOGETHER
 gff3head=$(head -n 3 ./$outdir/query.0.gff3)

diff --git a/5.45-80/iprs_wrapper.sh b/5.45-80/iprs_wrapper.sh
@@ -224,11 +224,14 @@ find /data/$outdir  -type f -name "query.*.tsv" -print0 | xargs -0 cat -- >> /da
 find /data/$outdir  -type f -name "query.*.json" -print0 | xargs -0 cat -- >> /data/$outdir/"$inname"'.json'
 
 
-##REMOVE XML HEADERLINES AND CAT FILES TOGETHER
+##REMOVE XML HEADERLINES TAILLINES AND CAT FILES TOGETHER
 xmlhead=$(head -n 1 /data/$outdir/query.0.xml)
+xmltail=$(tail -1 /data/$outdir/query.0.xml)
 find /data/$outdir  -type f -name "query.*.xml" -exec sed -i '1d' {} \;
+find /data/$outdir  -type f -name "query.*.xml" -exec sed -i '$d' {} \;
 find /data/$outdir  -type f -name "query.*.xml" -print0 | xargs -0 cat -- >> /data/$outdir/tmp.xml
 echo -e "$xmlhead" | cat - /data/$outdir/tmp.xml > /data/$outdir/"$inname"'.xml'
+echo -e "$xmltail" >>  /data/$outdir/"$inname"'.xml'
 
 
 ##REMOVE GFF# HEADERLINES AND CAT FILES TOGETHER